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9951 (T > C)

General info

Mitimpact ID
MI.8236
Chr
chrM
Start
9951
Ref
T
Alt
C
Gene symbol
MT-CO3 Extended gene annotation
Gene position
745
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
TGA/CGA
AA pos
249
AA ref
W
AA alt
R
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9951T>C
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
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Conservation

PhyloP 100v
7.67 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.951 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Pathogenic Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
.
fathmm
.
AlphaMissense
Likely pathogenic Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
.
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
High impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
9951T>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0082%
MITOMAP General GenBank Seqs
5
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

9951 (T > G)

General info

Mitimpact ID
MI.8237
Chr
chrM
Start
9951
Ref
T
Alt
G
Gene symbol
MT-CO3 Extended gene annotation
Gene position
745
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
TGA/GGA
AA pos
249
AA ref
W
AA alt
G
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9951T>G
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.67 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.951 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Pathogenic Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
.
fathmm
.
AlphaMissense
Likely pathogenic Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
High Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus+ Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
High impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
9951T>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.
~ 9951 (T/C) 9951 (T/G)
~ 9951 (TGA/CGA) 9951 (TGA/GGA)
MitImpact id MI.8236 MI.8237
Chr chrM chrM
Start 9951 9951
Ref T T
Alt C G
Gene symbol MT-CO3 MT-CO3
Extended annotation mitochondrially encoded cytochrome c oxidase III mitochondrially encoded cytochrome c oxidase III
Gene position 745 745
Gene start 9207 9207
Gene end 9990 9990
Gene strand + +
Codon substitution TGA/CGA TGA/GGA
AA position 249 249
AA ref W W
AA alt R G
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516050 516050
HGVS NC_012920.1:g.9951T>C NC_012920.1:g.9951T>G
HGNC id 7422 7422
Respiratory Chain complex IV IV
Ensembl gene id ENSG00000198938 ENSG00000198938
Ensembl transcript id ENST00000362079 ENST00000362079
Ensembl protein id ENSP00000354982 ENSP00000354982
Uniprot id P00414 P00414
Uniprot name COX3_HUMAN COX3_HUMAN
Ncbi gene id 4514 4514
Ncbi protein id YP_003024032.1 YP_003024032.1
PhyloP 100V 7.67 7.67
PhyloP 470Way 0.666 0.666
PhastCons 100V 1 1
PhastCons 470Way 0.951 0.951
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0
SIFT neutral neutral
SIFT score 0.05 0.05
SIFT4G Damaging Damaging
SIFT4G score 0.0 0.0
VEST Pathogenic Pathogenic
VEST pvalue 0.04 0.04
VEST FDR 0.35 0.35
Mitoclass.1 damaging damaging
SNPDryad Pathogenic Pathogenic
SNPDryad score 0.99 0.98
MutationTaster . .
MutationTaster score . .
MutationTaster converted rankscore . .
MutationTaster model . .
MutationTaster AAE . .
fathmm . .
fathmm score . .
fathmm converted rankscore . .
AlphaMissense likely_pathogenic likely_pathogenic
AlphaMissense score 0.9988 0.9635
CADD Deleterious Deleterious
CADD score 3.690896 4.005768
CADD phred 23.3 23.6
PROVEAN Damaging Damaging
PROVEAN score -12.02 -11.16
MutationAssessor . high
MutationAssessor score . 4.585
EFIN SP Damaging Damaging
EFIN SP score 0.484 0.596
EFIN HD Damaging Neutral
EFIN HD score 0.164 0.374
MLC Deleterious Deleterious
MLC score 0.58657734 0.58657734
PANTHER score . .
PhD-SNP score . .
APOGEE1 Neutral Neutral
APOGEE1 score 0.41 0.36
APOGEE2 VUS VUS+
APOGEE2 score 0.491777835176347 0.567677049195964
CAROL deleterious deleterious
CAROL score 1.0 1.0
Condel neutral neutral
Condel score 0.03 0.03
COVEC WMV deleterious deleterious
COVEC WMV score 2 2
MtoolBox deleterious deleterious
MtoolBox DS 0.81 0.81
DEOGEN2 . .
DEOGEN2 score . .
DEOGEN2 converted rankscore . .
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -3.78 -3.78
SIFT_transf medium impact medium impact
SIFT transf score -0.54 -0.54
MutationAssessor transf high impact high impact
MutationAssessor transf score 2.38 2.38
CHASM Neutral Neutral
CHASM pvalue 0.09 0.05
CHASM FDR 0.8 0.8
ClinVar id . .
ClinVar Allele id . .
ClinVar CLNDISDB . .
ClinVar CLNDN . .
ClinVar CLNSIG . .
MITOMAP Disease Clinical info . .
MITOMAP Disease Status . .
MITOMAP Disease Hom/Het ./. ./.
MITOMAP General GenBank Freq 0.0082% .
MITOMAP General GenBank Seqs 5 .
MITOMAP General Curated refs . .
MITOMAP Variant Class polymorphism .
gnomAD 3.1 AN . .
gnomAD 3.1 AC Homo . .
gnomAD 3.1 AF Hom . .
gnomAD 3.1 AC Het . .
gnomAD 3.1 AF Het . .
gnomAD 3.1 filter . .
HelixMTdb AC Hom . .
HelixMTdb AF Hom . .
HelixMTdb AC Het . .
HelixMTdb AF Het . .
HelixMTdb mean ARF . .
HelixMTdb max ARF . .
ToMMo 54KJPN AC . .
ToMMo 54KJPN AF . .
ToMMo 54KJPN AN . .
COSMIC 90 . .
dbSNP 156 id . .
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
For more info, please check the output legend.
0
Details:
0
Score:  
0
  [min -20, max 10]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min -20, max 12]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.7
  • Conserved:  score > 0.7 (soft threshold)
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.7
  • Conserved:  score > 0.7 (soft threshold)
Score:  
0
  [min 0, max 1]
  • Neutral:  score <= 0.15
  • Possibly damaging:  0.15 < score <= 0.85
  • Probably damaging:  score > 0.85
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.05
  • Deleterious:  score <= 0.05
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.05
  • Deleterious:  score <= 0.05
Score:  
0
  [min -16.13, max 10.64]
  • Neutral:  score > 1.5
  • Deleterious:  score <= 1.5
Score:  
0
  [min 0.0, max 1.0]
  • Likely benign:  score <= 0.34
  • Ambiguous:  0.34 < score < 0.56
  • Likely pathogenic:  score >= 0.56
Score:  
0
  [min -14, max 14]
  • Neutral:  score > -2.5
  • Deleterious:  score <= -2.5 (soft threshold)
Score:  
0
  [min -6, max 6]
  • Neutral:  score <= 0.8
  • Low impact:  0.8 < score <= 1.9
  • Medium impact:  1.9 < score <= 3.5
  • High impact:  score > 3.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.6
  • Damaging:  score <= 0.6
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.28
  • Damaging:  score <= 0.28
Phred score:  
0
  [min 0, max Unlimited]
  • Neutral:  score < 20 (soft threshold)
  • Deleterious:  score >= 20
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5 (soft threshold)
  • Deleterious:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Polymorphism:  score < 0.5
  • Disease causing:  score >= 0.5
P-value:  
0
  [min 0, max 1]
  • Neutral:  p-value > 0.05
  • Pathogenic:  p-value <= 0.05
Score:  
0
  [min 0, max 1]
No hard-thresholds were indicated by authors (ref). Indicatively:
  • Neutral:  score < 0.9
  • Pathogenic:  score >= 0.9
No score. Categorical only
Please refer to Additional File 14: Table S10 for further details.
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.98
  • Deleterious:  score >= 0.98
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
Score:  
0
  [min -6, max 6]
  • Neutral:  score < 0
  • Deleterious:  score > 0
  • Inaccurate prediction:  score = 0
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
DS score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.43
  • Deleterious:  score >= 0.43
Pathogenicity score:  
0
  [min 0, max 1]
  • Neutral:  score ≤ 0.5
  • Pathogenic:  score > 0.5


Pathogenicity score for this variant:  
0
  [min 0, max 1]
ACMG-AMP curations for mitochondrial variants should use the raw scores. Standalone probabilities are shown below:
  • Benign:  score ≤ 0.062 (prob. ≤ 0.001)
  • Likely-benign:  0.062 < score ≤ 0.265 (0.001 < prob. ≤ 0.1)
  • Low-scoring VUS (VUS-):  0.265 < score ≤ 0.396 (0.1 < prob. ≤ 0.33)
  • VUS:  0.396 < score ≤ 0.544 (0.33 < prob. ≤ 0.66)
  • High-scoring VUS (VUS+):  0.544 < score < 0.716 (0.66 < prob. < 0.9)
  • Likely-pathogenic:  0.716 ≤ score < 0.907 (0.9 ≤ prob. < 0.99)
  • Pathogenic:  score ≥ 0.907 (prob. ≥ 0.99)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1 (soft threshold)
  • Medium impact:  -1 < score < 1.5 (soft threshold)
  • High impact:  score >= 1.5 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
P-value:  
0
  [min 0, max 1]
  • Neutral:  FDR > 0.2
  • Driver:  FDR <= 0.2
The frequency of a CPD variant is proportional to the
number of aligned orthologous sequences that
carry a specific human pathogenic variant as
wild-type amino acid on the total number of aligned
sequences.

For more info, please check the output legend